tbuckley/cabot-search huggingface dataset:
DEBBIE: The Open Access Database of Experimental Scaffolds and Biomaterials Built Using an Automated Text Mining Pipeline
Authors: Javier O. Corvi, Austin McKitrick, José M. Fernández, Carla V. Fuenteslópez, Josep L. Gelpí, Maria‐Pau Ginebra, Salvador Capella‐Gutierrez, Osnat Hakimi
Journal: Advanced Healthcare Materials (2023)

Biomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools are becoming essential to overcome this information overload. Among them, text mining systems present an attractive option for the automated extraction of information from text documents into structured datasets. This work presents the first automated system for biomaterial related information extraction from the National Library of Medicine's premier bibliographic database (MEDLINE) research abstracts into a searchable database. The system is a text mining pipeline that periodically retrieves abstracts from PubMed and identifies research and clinical studies of biomaterials. Thereafter, the pipeline identifies sixteen concept types of interest in the abstract using the Biomaterials Annotator, a tool for biomaterials Named Entity Recognition (NER). These concepts of interest, along with the abstract and relevant metadata are then deposited in DEBBIE, the Database of Experimental Biomaterials and their Biological Effect. DEBBIE is accessible through a web application that provides keyword searches and displays results in an intuitive and meaningful manner, aiming to facilitate an efficient mapping and organization of biomaterials information.
Langerhans Cell Histiocytosis Showed Intense Uptake of 68Ga-FAPI
Authors: Qingqing Pan, Hongzhe Zhang, Xinxin Cao, Jian Li, Yaping Luo
Journal: Clinical Nuclear Medicine (2023)

Abstract A 23-year-old man was recently diagnosed with Langerhans cell histiocytosis (LCH). 68 Ga-FAPI PET/CT showed multiple lesions with intense FAPI uptake in the axial and appendicular skeleton with lytic or mixed bone destruction, consistent with osseous lesions of LCH. FAPI-avid foci around the right atrium and inferior vena cava, as well as micronodules and thin-walled cysts in the lungs, were also noted, possibly also involvement of LCH. This case suggested that 68 Ga-FAPI PET/CT may have the potential to be applied in evaluation of LCH.
Integrating Opioid Use Disorder Treatment Into Primary Care Settings
Authors: Elizabeth J. Austin, Jessica Chen, Elsa S. Briggs, Lori Ferro, Paul Barry, Ashley Heald, Joseph O. Merrill, Geoffrey M. Curran, Andrew J. Saxon, John C. Fortney, Anna D. Ratzliff, Emily C. Williams
Journal: JAMA Network Open (2023)

Medication for opioid use disorder (MOUD) (eg, buprenorphine and naltrexone) can be offered in primary care, but barriers to implementation exist.To evaluate an implementation intervention over 2 years to explore experiences and perspectives of multidisciplinary primary care (PC) teams initiating or expanding MOUD.This survey-based and ethnographic qualitative study was conducted at 12 geographically and structurally diverse primary care clinics that enrolled in a hybrid effectiveness-implementation study from July 2020 to July 2022 and included PC teams (prescribing clinicians, nonprescribing behavioral health care managers, and consulting psychiatrists). Survey data analysis was conducted from February to April 2022.Implementation intervention (external practice facilitation) to integrate OUD treatment alongside existing collaborative care for mental health services.Data included (1) quantitative surveys of primary care teams that were analyzed descriptively and triangulated with qualitative results and (2) qualitative field notes from ethnographic observation of clinic implementation meetings analyzed using rapid assessment methods.Sixty-two primary care team members completed the survey (41 female individuals [66%]; 1 [2%] American Indian or Alaskan Native, 4 [7%] Asian, 5 [8%] Black or African American, 5 [8%] Hispanic or Latino, 1 [2%] Native Hawaiian or Other Pacific Islander, and 46 [4%] White individuals), of whom 37 (60%) were between age 25 and 44 years. An analysis of implementation meetings (n = 362) and survey data identified 4 themes describing multilevel factors associated with PC team provision of MOUD during implementation, with variation in their experience across clinics. Themes characterized challenges with clinical administrative logistics that limited the capacity to provide rapid access to care and patient engagement as well as clinician confidence to discuss aspects of MOUD care with patients. These challenges were associated with conflicting attitudes among PC teams toward expanding MOUD care.The results of this survey and qualitative study of PC team perspectives suggest that PC teams need flexibility in appointment scheduling and the capacity to effectively engage patients with OUD as well as ongoing training to maintain clinician confidence in the face of evolving opioid-related clinical issues. Future work should address structural challenges associated with workload burden and limited schedule flexibility that hinder MOUD expansion in PC settings.
FDA Aims to Broaden Access to New Therapies
Journal: Cancer Discovery (2023)

Abstract The FDA is ramping up Project FrontRunner, which urges drugmakers to seek accelerated approval of experimental drugs as first-line treatments for patients with advanced or metastatic disease, rather than focusing on patients who have tried multiple therapies and/or exhausted available options. Experts say the program has the potential to expand access while improving the risk–benefit assessment of new drugs by initiating randomized controlled trials earlier in the drug development process.
Anesthesia Clinical Workload Estimated From Electronic Health Record Documentation vs Billed Relative Value Units
Authors: Sunny S. Lou, Laura R. Baratta, Daphne Lew, Derek Harford, Michael S. Avidan, Thomas Kannampallil
Journal: JAMA Network Open (2023)

Accurate measurements of clinical workload are needed to inform health care policy. Existing methods for measuring clinical workload rely on surveys or time-motion studies, which are labor-intensive to collect and subject to biases.To compare anesthesia clinical workload estimated from electronic health record (EHR) audit log data vs billed relative value units.This cross-sectional study of anesthetic encounters occurring between August 26, 2019, and February 9, 2020, used data from 8 academic hospitals, community hospitals, and surgical centers across Missouri and Illinois. Clinicians who provided anesthetic services for at least 1 surgical encounter were included. Data were analyzed from January 2022 to January 2023.Anesthetic encounters associated with a surgical procedure were included. Encounters associated with labor analgesia and endoscopy were excluded.For each encounter, EHR-derived clinical workload was estimated as the sum of all EHR actions recorded in the audit log by anesthesia clinicians who provided care. Billing-derived clinical workload was measured as the total number of units billed for the encounter. A linear mixed-effects model was used to estimate the relative contribution of patient complexity (American Society of Anesthesiology [ASA] physical status modifier), procedure complexity (ASA base unit value for the procedure), and anesthetic duration (time units) to EHR-derived and billing-derived workload. The resulting β coefficients were interpreted as the expected effect of a 1-unit change in each independent variable on the standardized workload outcome. The analysis plan was developed after the data were obtained.A total of 405 clinicians who provided anesthesia for 31 688 encounters were included in the study. A total of 8 288 132 audit log actions corresponding to 39 131 hours of EHR use were used to measure EHR-derived workload. The contributions of patient complexity, procedural complexity, and anesthesia duration to EHR-derived workload differed significantly from their contributions to billing-derived workload. The contribution of patient complexity toward EHR-derived workload (β = 0.162; 95% CI, 0.153-0.171) was more than 50% greater than its contribution toward billing-derived workload (β = 0.106; 95% CI, 0.097-0.116; P < .001). In contrast, the contribution of procedure complexity toward EHR-derived workload (β = 0.033; 95% CI, 0.031-0.035) was approximately one-third its contribution toward billing-derived workload (β = 0.106; 95% CI, 0.104-0.108; P < .001).In this cross-sectional study of 8 hospitals, reimbursement for anesthesiology services overcompensated for procedural complexity and undercompensated for patient complexity. This method for measuring clinical workload could be used to improve reimbursement valuations for anesthesia and other specialties.
Dupilumab significantly improves sleep in adults with atopic dermatitis: results from the 12-week placebo-controlled period of the 24-week phase IV randomized double-blinded placebo-controlled DUPISTAD study
Authors: Joseph F Merola, Albert S Chiou, Emmanuel During, Antonio Costanzo, Peter Foley, Amani Alfalasi, Shaila Gogate, Andreas Pinter, Roni Dodiuk-Gad, Dagmar Simon, Marie Tauber, Richard Weller, Jose-Juan Pereyra-Rodriguez, Marius Ardeleanu, Jiangming Wu, Zafer E Ozturk
Journal: British Journal of Dermatology (2023)

Sleep disturbance is a prominent symptom of atopic dermatitis (AD) and can result in insomnia, daytime fatigue, drowsiness, reduced productivity and impaired quality of life (QoL). The Dupilumab Effect on Sleep in AD Patients (DUPISTAD) phase IV randomized double-blinded placebo-controlled study evaluated the impact of dupilumab treatment on sleep and other patient- and physician-reported outcomes. Adults with moderate-to-severe AD were randomized 2 : 1 to dupilumab 300 mg once every 2 weeks (q2w) or placebo for 12 weeks; concomitant topical corticosteroids were permitted. Patients subsequently entered an open-label phase and received dupilumab 300 mg q2w for a further 12 weeks. The primary endpoint was the percentage change in sleep quality from baseline to week 12, assessed using a novel numeric rating scale (NRS). Secondary and exploratory endpoints included percentage change in peak pruritus NRS (PP NRS), change in SCORing Atopic Dermatitis (SCORAD), SCORAD sleep visual analogue scale (VAS), Eczema Area and Severity Index, Patient-Reported Outcomes Measurement Information System (PROMIS) sleep-related impairment T-score and the Epworth Sleepiness Scale. Sleep diary and wrist actigraphy measurements were recorded throughout the study. In total, 127 patients received dupilumab and 61 patients received placebo. Demographic and baseline disease characteristics were balanced between groups. Sleep quality NRS significantly improved in patients treated with dupilumab by week 12 vs. placebo [least squares mean of the difference (LSMD) -15.5%, P < 0.001]. PP NRS (LSMD -27.9%, P < 0.001), SCORAD (LSMD -15.1, P < 0.001), SCORAD sleep VAS (LSMD -2.1, P < 0.001) and PROMIS T-score (LSMD -3.6, P < 0.001) were also significantly improved at week 12 with dupilumab vs. placebo. The overall percentage of patients reporting treatment-emergent adverse events was lower in the dupilumab group (56.7%) than in the placebo group (67.2%). Dupilumab significantly improved sleep quality and perception of sleep continuity, itch, metrics of AD severity and QoL in adults with moderate-to-severe AD, with an acceptable safety profile compared with placebo.
American Football Play and Parkinson Disease Among Men
Authors: Hannah J. Bruce, Yorghos Tripodis, Michael McClean, Monica Korell, Caroline M. Tanner, Brittany Contreras, Joshua Gottesman, Leslie Kirsch, Yasir Karim, Brett Martin, Joseph Palmisano, Bobak Abdolmohammadi, Ludy C. Shih, Thor D. Stein, Robert A. Stern, Charles H. Adler, Jesse Mez, Chris Nowinski, Ann C. McKee, Michael L. Alosco
Journal: JAMA Network Open (2023)

Parkinsonism and Parkinson disease (PD) are known to result from repetitive head impacts from boxing. Repetitive head impacts from American football may also be associated with increased risk of neurodegenerative pathologies that cause parkinsonism, yet in vivo research on the association between football play and PD is scarce and limited by small samples and equivocal findings.
68Ga-DOTA-FAPI-04 Imaging of Bilateral Phyllodes Tumor
Authors: Göksel Alçın, Esra Arslan, Melis Baykara Ulusan, Tamer Aksoy, Nurhan Ergül, Tevfik Fikret Çermik
Journal: Clinical Nuclear Medicine (2023)

Abstract We present a case of bilateral Phyllodes tumor located in both breasts in a 41-year-old woman who was detected with increased uptake on 68 Ga-FAPI-04 (fibroblast activation protein inhibitor) and 18 F-FDG PET/CT imaging. The tumor filling up the right breast was identified as borderline Phyllodes. The tumor with mild uptake in the left breast was reported as a benign Phyllodes tumor.
Imaging the impact of blood-brain barrier disruption induced by focused ultrasound on P-glycoprotein function
Authors: Sébastien Goutal, Anthony Novell, Sarah Leterrier, Louise Breuil, Erwan Selingue, Matthieu Gerstenmayer, Solène Marie, Bruno Saubaméa, Fabien Caillé, Oliver Langer, Charles Truillet, Benoît Larrat, Nicolas Tournier
Journal: Journal of Controlled Release (2023)
Public Attitudes About the Use of Gene Therapy in Mainland China
Authors: Yiqi Li, Xinyue Zhang, Ze Xiang, Tianle Chen, Zihao Hu, Kexin Yang, Xinying Sun, Yibo Wu, Jian Wu
Journal: JAMA Network Open (2023)

In addition to technical barriers, public attitudes about the use of gene therapy have an important association with the clinical implementation of gene therapy.
Local delivery of hrBMP4 as an anticancer therapy in patients with recurrent glioblastoma: a first-in-human phase 1 dose escalation trial
Authors: Eelke M. Bos, Elena Binda, Iris S.C. Verploegh, Eva Wembacher, Daphna Hoefnagel, Rutger K. Balvers, Anne L. Korporaal, Andrea Conidi, Esther A. H. Warnert, Nadia Trivieri, Alberto Visioli, Paola Zaccarini, Laura Caiola, Rogier van Wijck, Peter van der Spek, Danny Huylebroeck, Sieger Leenstra, Martine L.M. Lamfers, Zvi Ram, Manfred Westphal, David Noske, Federico Legnani, Francesco DiMeco, Angelo Luigi Vescovi, Clemens M.F. Dirven
Journal: Molecular Cancer (2023)

This Phase 1 study evaluates the intra- and peritumoral administration by convection enhanced delivery (CED) of human recombinant Bone Morphogenetic Protein 4 (hrBMP4) - an inhibitory regulator of cancer stem cells (CSCs) - in recurrent glioblastoma.In a 3 + 3 dose escalation design, over four to six days, fifteen recurrent glioblastoma patients received, by CED, one of five doses of hrBMP4 ranging from 0·5 to 18 mg. Patients were followed by periodic physical, neurological, blood testing, magnetic resonance imaging (MRI) and quality of life evaluations. The primary objective of this first-in-human study was to determine the safety, dose-limiting toxicities (DLT) and maximum tolerated dose (MTD) of hrBMP4. Secondary objectives were to assess potential efficacy and systemic exposure to hrBMP4 upon intracerebral infusion.Intra- and peritumoral infusion of hrBMP4 was safe and well-tolerated. We observed no serious adverse events related to this drug. Neither MTD nor DLT were reached. Three patients had increased hrBMP4 serum levels at the end of infusion, which normalized within 4 weeks, without sign of toxicity. One patient showed partial response and two patients a complete (local) tumor response, which was maintained until the most recent follow-up, 57 and 30 months post-hrBMP4. Tumor growth was inhibited in areas permeated by hrBMP4.Local delivery of hrBMP4 in and around recurring glioblastoma is safe and well-tolerated. Three patients responded to the treatment. A complete response and long-term survival occurred in two of them. This warrants further clinical studies on this novel treatment targeting glioblastoma CSCs.ClinicaTrials.gov identifier: NCT02869243.
SARS-CoV-2 Infection and Death Rates Among Maintenance Dialysis Patients During Delta and Early Omicron Waves — United States, June 30, 2021–September 27, 2022
Authors: Jose Navarrete, Gregory Barone, Iram Qureshi, Austin Woods, Kira Barbre, Lu Meng, Shannon Novosad, Qunna Li, Minn Minn Soe, Jonathan Edwards, Emily Wong, Hannah E. Reses, Sydney Guthrie, John Keenan, Leticia Lamping, Meeyoung Park, Sorie Dumbuya, Andrea L. Benin, Jeneita Bell
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Persons receiving maintenance dialysis are at increased risk for SARS-CoV-2 infection and its severe outcomes, including death. However, rates of SARS-CoV-2 infection and COVID-19-related deaths in this population are not well described. Since November 2020, CDC's National Healthcare Safety Network (NHSN) has collected weekly data monitoring incidence of SARS-CoV-2 infections (defined as a positive SARS-CoV-2 test result) and COVID-19-related deaths (defined as the death of a patient who had not fully recovered from a SARS-CoV-2 infection) among maintenance dialysis patients. This analysis used NHSN dialysis facility COVID-19 data reported during June 30, 2021-September 27, 2022, to describe rates of SARS-CoV-2 infection and COVID-19-related death among maintenance dialysis patients. The overall infection rate was 30.47 per 10,000 patient-weeks (39.64 among unvaccinated patients and 27.24 among patients who had completed a primary COVID-19 vaccination series). The overall death rate was 1.74 per 10,000 patient-weeks. Implementing recommended infection control measures in dialysis facilities and ensuring patients and staff members are up to date with recommended COVID-19 vaccination is critical to limiting COVID-19-associated morbidity and mortality.
Interdisciplinary Analyses of Bronze Age Communities from Western Hungary Reveal Complex Population Histories
Authors: Dániel Gerber, Bea Szeifert, Orsolya Székely, Balázs Egyed, Balázs Gyuris, Julia I Giblin, Anikó Horváth, Kitti Köhler, Gabriella Kulcsár, Ágnes Kustár, István Major, Mihály Molnár, László Palcsu, Vajk Szeverényi, Szilvia Fábián, Balázs Gusztáv Mende, Mária Bondár, Eszter Ari, Viktória Kiss, Anna Szécsényi-Nagy
Journal: Molecular Biology and Evolution (2023)

In this study, we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archeological cultures (3,530-1,620 cal Bce). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted Pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture-associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture-related population and one from a previously unrecognized source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted Pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analyzing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.
Salpingectomy and the Risk of Ovarian Cancer in Ontario
Authors: Vasily Giannakeas, Ally Murji, Lorraine L. Lipscombe, Steven A. Narod, Joanne Kotsopoulos
Journal: JAMA Network Open (2023)

A body of pathological and clinical evidence supports the position that the fallopian tube is the site of origin for a large proportion of high-grade serous ovarian cancers. Consequently, salpingectomy is now considered for permanent contraception (in lieu of tubal ligation) or ovarian cancer prevention (performed opportunistically at the time of surgical procedures for benign gynecologic conditions).To evaluate the association between salpingectomy and the risk of invasive epithelial ovarian, fallopian tube, and peritoneal cancer.This population-based retrospective cohort study included all women aged 18 to 80 years who were eligible for health care services in Ontario, Canada. Participants were identified using administrative health databases from Ontario between January 1, 1992, and December 31, 2019. A total of 131 516 women were included in the primary (matched) analysis. Women were followed up until December 31, 2021.Salpingectomy (with and without hysterectomy) vs no pelvic procedure (control condition) among women in the general population.Women with a unilateral or bilateral salpingectomy in Ontario between April 1, 1992, and December 31, 2019, were matched 1:3 to women with no pelvic procedure from the general population. Cox proportional hazards regression models were used to estimate the hazard ratios (HRs) and 95% CIs for ovarian, fallopian tube, and peritoneal cancer combined.Among 131 516 women (mean [SD] age, 42.2 [7.6] years), 32 879 underwent a unilateral or bilateral salpingectomy, and 98 637 did not undergo a pelvic procedure. After a mean (range) follow-up of 7.4 (0-29.2) years in the salpingectomy group and 7.5 (0-29.2) years in the nonsurgical control group, there were 31 incident cancers (0.09%) and 117 incident cancers (0.12%), respectively (HR, 0.82; 95% CI, 0.55-1.21). The HR for cancer incidence was 0.87 (95% CI, 0.53-1.44) when comparing those with salpingectomy vs those with hysterectomy alone.In this cohort study, no association was found between salpingectomy and the risk of ovarian cancer; however, this observation was based on few incident cases and a relatively short follow-up time. Studies with additional years of follow-up are necessary to define the true level of potential risk reduction with salpingectomy, although longer follow-up will also be a challenge unless collaborative efforts that pool data are undertaken.
A Photopolymerizable Biocompatible Hyaluronic Acid Hydrogel Promotes Early Articular Cartilage Repair in a Minipig Model In Vivo
Authors: Liang Gao, Riccardo Beninatto, Tamás Oláh, Lars Goebel, Ke Tao, Rebecca Roels, Steffen Schrenker, Julianne Glomm, Jagadeesh K. Venkatesan, Gertrud Schmitt, Ebrar Sahin, Ola Dahhan, Mauro Pavan, Carlo Barbera, Alba Di Lucia, Michael D. Menger, Matthias W. Laschke, Magali Cucchiarini, Devis Galesso, Henning Madry
Journal: Advanced Healthcare Materials (2023)

Articular cartilage defects represent an unsolved clinical challenge. Photopolymerizable hydrogels are attractive candidates supporting repair. This study investigates the short-term safety and efficacy of two novel hyaluronic acid (HA)-triethylene glycol (TEG)-coumarin hydrogels photocrosslinked in situ in a clinically relevant large animal model. It is hypothesized that HA-hydrogel-augmented microfracture (MFX) is superior to MFX in enhancing early cartilage repair, and that the molar degree of substitution and concentration of HA affects repair. Chondral full-thickness defects in the knees of adult minipigs are treated with either 1) debridement (No MFX), 2) debridement and MFX, 3) debridement, MFX, and HA hydrogel (30% molar derivatization, 30 mg mL